I haven't seen the series at all, but it sounds like you may be describing Galaxy Express 999?

It's been a LONG time since I watched it... especially since it was never released on DVD... i do have an old VHS copy of it though... It sounds like you are looking for:

Galaxy Express 999

It both pirate queen Emereldas and Captain Herlock make an appearance, and it is centered around a human boy named Tetsuro and his travels with Maetel aboard the space train.

There was an anime series, a couple of movies, and manga.

You can watch the series, episodes 1-30, on Crunchyroll.

I found an old VHS copy of Galaxy Express 999 and thought that was it, but after watching it I realized it wasn't. Since then I've been dying to find it again. But thank you for taking the time to try for me!

I saw this particular one when I lived in Japan, so who knows? Maybe it never made it stateside. I can remember watching it around the same time Nausicaa: Valley of the Winds was released over there.

Well, Leiji Matsumoto (the creator of Galsxy Express 999) is famous for his space operas and quite a few have trains in space. You could skim his lists of works and see if any jumps out at you:

en.wikipedia.org/wiki/Leiji_Matsumoto

Okay, this has nothing to do with Sess/Kag, but we are all obviously anime fans and I'm wondering if anyone can tell me the name of this one. It's an older one. I saw it when I was around eight or so and so I'm dragging these images out of my mind but here's what I can remember:

There's a train that goes through space and a boy (i think it may just be a kid) is riding on it. Anyhoo, the train goes to all these different worlds. One of the worlds a storm came through a turned everyone to stone except this one guy who guards all the other stone people (and especially his girlfriend) from pirates. Another scene of the movie is a bunch of babies who died being let out into space (sounds gruesome, but the scene was actually very sad and remembering).

That's all I can remember, but I really liked this one when I was a kid and I wouldn't mind seeing it again. Any help would be appreciated.